My TARDIS
by Nicolas Cofield
Summary: One Doctor...One TARDIS...and a whole Universe of trouble. After the loss of his TARDIS, the Doctor must come to terms with the things he has been fleeing from: his choices. Book 1 of Series 1-Destiny (Story complete, so please review.)
1. Chapter One- A Warning

Disclaimer: I in no way, shape, or form own the _Doctor Who _series and the _characters _within thereof.

A/N- This will be my first work of fanfiction, so please read the other chapters before making up your mind about this story.

**Chapter One- A Warning**

_(October, in the near distant future…)_

In a city awash with lights, the Doctor and the Ponds found themselves at peace in the city of Paris, France. Emerging from the TARDIS, the Doctor took a few steps out and began spinning with a smile on his face. "In a city with so much to do, what's one to do," he said.

Amy and Rory Pond just stood in awe of all the beauty around them. The Doctor just stood with his hand on his sides, smiling as Rory and Amy talked about what they wanted to do. "I suggest we go to the Botanical Gardens," Rory announced to the Doctor.

"I don't have a problem with that," the Doctor said as he began walking, "all except for orchids. I hate orchids with their orchid selves." The Doctor quickly turned back to lock the TARDIS before he continued his stroll with the Ponds.

While the Ponds relaxed in a hotel, the Doctor went out for a stroll on his own. With a newly acquired fez, he went to the destination he had been told to go. From the lights of the Fontaine de la Pyramide, he waited as he was instructed to. He propped himself up against a wall and whistled a few lines of the French National Anthem.

"Still remember the time that you helped storm the Bastille," another person propped beside him said.

"The Cybermen never saw it coming..."

"And neither have you,"

The Doctor suddenly had his sonic screwdriver out and pointed at the individual. "What are you talking about?"

"You can put the sonic away. I will die in the next ninety seconds and I have vital information to give to you."

The Doctor put it back in his coat pocket and crossed his arms. "I'm tired of seeing death," he muttered bitterly.

The man doubled over, clenching his side with one hand. The Doctor was immediately at his side. "Speak your piece," he whispered. The man began coughing, then wheezing violently. He put his hands on the Doctor's shoulders and began speaking.

"Darkness shall fall," he whispered. "All the people you hold dear will be consumed by the Darkness. You shall seek death, yet it will flee from you. Through strength, you shall find help from it that was lost…" The man then screamed and grabbed for his heart. With his last dying breath, he produced a pouch and thrust it into the Doctor's hands. "Run," the man said before he died.


	2. Chapter Two- Darkness Descends

Disclaimer: I in no way, shape, or form own the _Doctor Who _series and the _characters _therein.

A/N- This will be my first try at doing fanfiction. Please tell me if you think there is any room for improvement.

**Chapter Two- Darkness Descends **

"So you're telling me that this guy who knew you from the French Revolution instructs you to meet him, starts dying, and then hands you a pouch with who-knows-what in it," Amy said to the Doctor as he stood over her and Rory's table, "right when he dies and you now want to leave?"

"You have to listen," the Doctor said. "Your lives could be at risk."

"Aren't they always?" Rory asked as he took a drink from his wine glass. "Doctor, we've always been in some sort of danger around you. Everything has been fine and will continue to be so."

"But you just don't understand, do you?!" the Doctor shouted. "After the whole prison ship fiasco, I knew I should've let you guys go, but something told me not to. Now, I regret making that decision."

Amy whispered a few words to Rory; he nodded and she took the Doctor by the arm and onto a balcony.

"What did the man say to you?" she asked the Doctor. "The truth," he answered.

"Doctor, you are the nicest man I've ever met. You are wonderful and brilliant beyond your years. Whatever he said or told you it's…"

"Doctor!" interrupted Rory. "Why's the sky dark at 1:58 p.m.?" The Doctor instead grabbed both of them by the wrist instead of answering them. With a few lowly shouts of protest from Rory, the Doctor and the Ponds were safe in the TARDIS.

"What the bloody 'ell was that?" sneered Amy in her strongest Scottish accent.

"The shadows… they don't eat people, so it isn't Vashta Neradan," the Doctor said without acknowledging Amy's inquiry. He searched the databanks for "The Darkness", finding nothing.

"We...are…leaving" the Doctor said as he began operating the controls. Rory tried to put his hands on him to calm him down but the Doctor shoved him away.

"What has gotten into you?" Rory shouted as the TARDIS began whirling through the Time Vortex.

"I have to get you to safety!" the Doctor shouted. The TARDIS continued forward with much difficulty as it fought off the "Darkness". The readout screen above the controls registered nothing. In his mind, the Doctor knew that this would be the last time he would see the Ponds for a very long time.

Suddenly, the TARDIS became still. The Doctor threw them a few bags and screamed for them to run.

"But why must we leave?" Amy shouted to the Doctor.

"For your lives!" the Doctor said as the TARDIS doors closed by themselves. He was sent flying into the railings with nothing but the bars for support. The Darkness had somehow grabbed the TARDIS and was trying to send it somewhere. His head hit the bars and everything went black.


	3. Chapter Three- Found

Disclaimer: I in no way, shape, or form own the _Doctor Who _series and the _characters _therein.

A/N- This will be my first try at doing fanfiction. Please tell me if you think there is anything else I should include in the plot.

**Chapter Three- Found**

The Doctor groggily awoke to his eyes looking up at the TARDIS control panel being upside down. He attempted to regain his composure which, to his surprise, came back way too fast. His hands, momentarily covered with scars, soon disappeared as he looked down at them. The Doctor knew that his time was ending.

He got up as fast as he could and went to the doors. Opening it, he collapsed onto the ground as the first pains of regeneration hit him. He looked up, not into the sky, but into the sharp multicolored eyes of a red-cloaked individual.

"The Champion of Time, reduced to nothing but a scorched lump of flesh, clothes, and broken dreams,"  
the individual said. "Worry not, Doctor. Your time is still to come." The individual put out its hand and placed it on the Doctor's shoulder. The Doctor's pain came back momentarily, and then stopped completely.

"Why do you do this?" the Doctor asked.

"Truth be told," it answered," I need your TARDIS." The Doctor tried to stop it, but was repelled by an invisible barrier.

"You can't," the Doctor yelled as the figure stepped through the TARDIS doors. "She's the only thing I have!" The TARDIS began blinking out of existence until it disappeared completely. The Doctor, heart filled with sorrow, closed his eyes and disappeared.

_**(December 2**__**nd**__**, 1697: Saint Paul's Cathedral)**_

St. Paul's Cathedral had been completed exactly ten years ago and today the great and good of London gathered for a special service to celebrate the anniversary. Everyone present was dressed in their finest attire as benefited the event, that is all except for one man. This man was dressed like no other in the assembled crowd. In a top-hat, suit with tails, and carrying swagger stick, the individual walked past a priest and dropped a bag containing pure silver coins into his hand. The priest only grasped for air as the man was engulfed in the crowd of people entering the church.

The Doctor took a seat at a pew furthest from the altar. Every Sunday, he would find a church of some sort and donate a little bit of the wealth he had acquired in his time of being moored in late 17th Century London. Through sermons, he received nothing of the message, but instead a nagging guilt. In his mind, he could see the Pond's living life to the fullest; his other friends in the universe would also be safe from him.

On this special day, though, preaching the gospel wouldn't be at the top of them agenda. Today, someone was being honored for their service.

"And on this day," the priest at the altar said," we would like to honor one of the great pillars of the community. Inspector, would you please stand up."

The Doctor got up from his seat reluctantly, and strode down the massive aisle to the front of the altar. After much applause, he received his plaque and went back to his seat. After service, the Doctor was stopped by a short and stout individual in a carriage.

"Doctor… or is it Inspector," the individual asked from the window of his carriage.

"Depends on who's asking?" the Doctor replied. After being told to get in, the Doctor sat in one of the seats of the Carriage. Before the individual could say anything else, the Doctor pushed back its hood with his cane, revealing the face of a Sontaran.

"What?" the Doctor asked as the carriage disappeared from Earth.


	4. Chapter Four- The Inconvenient Truth Pt1

Disclaimer: I in no way, shape, or form own the _Doctor Who _series and the _characters _therein.

A/N- This will be my first try at doing fanfiction. Please tell me if you think there is anything else I should include in the plot.

**Chapter Four- The Inconvenient Truth (Part-1)**

"By order of Convention 15 of the Shadow Proclamation, I command at once to see your leader!" the Doctor yelled. The Sontaran grunts obliged, and led him into a room with a table in the center. The grunt saluted him and then left. The Doctor quickly got up and began scanning the room with his sonic cane.

"Well…" he said looking at the readings on the cane, "what does the Grand Strategic Council want with me?"

"Want we want, Doctor, is your help," said a Sontaran with his hand extended out. "I am Space Marshall Graflon."

"Pleased to meet you, Marshall," the Doctor said as he shook his hand.

"I'll over look that demotion in rank," the Marshall responded as he gestured to the Doctor to take a seat. Soon, other Sontarans filled up the seats. Marshall Graflon got up and addressed the group.

"As you may have well known, we are facing a threat that even our military might cannot quash. Our fleets' attempts to destroy it have been catastrophic to our cloning rates. Our all-powerful Imperator has asked that we bring in our worst enemy to help us: The Doctor."

Every one of them turned to look at the only humanoid at the table. He waved and smiled at all of them with content.

"Doctor," the Marshall continued, "we are very well aware of the loss of your TARDIS. We believe that this entity is using it to create a weapon that may very cause the destruction of the Universe, making this individual the Most Dangerous Person in the Universe. We intend to capture him and, in return for our past military engagements, trade him to the Shadow Proclamation for trial.

"And you will no doubt join him in his quest if they do not lead into your demands," the Doctor said as he put his foot up on the table. The Sontaran s said nothing to him. "Well, isn't that honorable?" The Marshall got up along with some of the Council with their weapons drawn.

"You Doctor," the Marshall said," are in no position to insult us."

"If you are aware of my TARDIS being gone, then you know that I have nothing to lose," the Doctor said. He got up and began making his way to the door when the ship suddenly shook.

"What have you done," the Marshall yelled as alarm sirens began going off. The Doctor said nothing and ran out. All over the ship, a breech in the hull near Section Seven was detected along with a life sign.

"Stop!" someone yelled.

The Doctor turned to look into the face of the woman he once knew as Jenny, his daughter.


	5. The Inconvenient Truth Pt2

Disclaimer: I in no way, shape, or form own the _Doctor Who _series and the _characters _therein.

A/N- This will be my first try at doing fanfiction. Please read other chapters before coming to a conclusion.

**The Inconvenient Truth (Part 2)**

"Where are we going," the Doctor asked as his daughter returned fire at the Sontaran troops. He wasn't really aware of whom she was, but she looked familiar. She threw a plasmid grenade down the corridor and pulled the Doctor into a side room.

"Doctor," she said as she sealed the door, "don't you recognize me?"

"I do," he said," but I don't. What are you doing on the flagship of the Sontaran Grand Strategic Council?"

"You may not remember it," she told him as she began splicing into the wires on the console, but when I died on Messaline, I wasn't exactly dead." She took a handheld from her bag and connected it to the mass of wires. "I took the rocket, and went out into the Universe to do well, just as you would. Through my adventures, I've heard whispers about you until a kind, one-armed priest told me of your good deeds…Inspector." She laughed and connected the last group of cables to the device, prompting a countdown timer to go off.

"I suggest you come with me," Jenny said. "I'd hate to lose my father again." The Doctor stood for a moment and smiled.

"Count me in," the Doctor said in his happiest voice. For the first time, he actually felt as if he had purpose. "What happens when the timer hits zero?"

"We'll use the blast to create a temporal shift and head forward to the present," she said to him as she linked the timer to a device on her arm.

The Doctor, not knowing why, hugged the girl.

"Well, how exactly do you suggest we get off of this rust bucket?" The Doctor asked as he scanned the room. "I'll just sonic this wall and go along from there," she answered. As they made their way through their makeshift escape route, the Sontarans had breached the door. By the time the Sontarans had figured out what happened, the Doctor and his daughter were well on their way to the flight bay.

"How are we going to keep this ship anchored in this timeline without it going with us," the Doctor asked. "Simple," Jenny said. "You just…"

"Use a slingshot effect," the Doctor yelled," which is brilliant!" The Doctor dead-locked the doors to the hangar bay and began overloading the gravity projectors. His plan was to create a bubble of gravity that would keep them in the Time Vortex without taking the ship. Jenny looked down at the time and nodded at the Doctor.

"It's time," she said as she put her arms around her father. The Sontarans entered the flight bay just as the charge went off. The Council had already left as the ship began coming apart. The barely functioning temporal engine parts in Jenny's rocket were ripped apart by the electrical current projected by the explosives. Jenny's wrist-mounted time-travel device sustained the field as both of them went hurling through time and towards the Earth. There was a momentary flash of light followed by an explosion.

The Doctor and Jenny, clothes smoking from the fresh landing of entering another time stream, stood in the living room of a house. Of all people, Rory Pond sat on the couch, face full of tears and tissues in on the ground from the shock.

"What happened?" the Doctor asked him.

"You liar!" he shouted. "Amy's dead because of you."

The Doctor sat down beside Rory and picked up a clock. The clock read 2:28 p.m. Year 2035.

"Jenny," the Doctor said, "I've been gone for twenty-six years…"


	6. Chapter Five- A Question

Disclaimer: I in no way, shape, or form own the _Doctor Who _series and the _characters _therein.

A/N- This will be my first try at doing fanfiction. Please read other chapters before coming to a conclusion.

**Chapter Five- A Question**

Jenny just stood there as Rory Pond angrily got up and began pacing the room, screaming at the Doctor like a mad man.

"When you left us, Amy was in shock for a whole month. She almost gave herself a heart attack trying to figure out how to help you. Life went on after that though; she even made a fragrance line trying to get your attention. 'For the girl who's tired of waiting' was the marketing slogan. Then we got a knock at our door from 'UNIT'." He stopped telling his story and instead began hitting the Doctor.

"Why are you just standing there and taking it?" Rory yelled. "Fight back!"

The Doctor just continued to stand still. Even in a different time stream, he couldn't keep his past from hurting them.

"She said those words," Rory spat at the Doctor. "He is the..."

"...Nicest man I've ever met. You are wonderful and brilliant beyond your years." The Doctor said finishing Rory's sentence for him. "How did she die?"

Rory finally understood how much pain the Doctor was in. He sat back down on the couch and silently apologized to Jenny. He looked outside the window and continued to tell the Doctor what had happened.

"UNIT has a plan. They were going to use the residual energy from Amy to make a time-traveling device. She volunteered to do it without asking any questions. I...I should've stopped her. The energy extrapolation procedures almost killed her alone. After ten whole years of experimentation, they finally had a device built. Something happened though...She took the thing and disappeared right in front of their eyes."

"Where did she go?" the Doctor asked. Jenny looked at him and saw that he had already figured it out.

"They said that she went into the Time Vortex itself with no way to navigate in it or even survive. The statistics of her survival were next to nothing they told me."

The Doctor suddenly fell to the floor. His mind went black and then foggy as the outline of a hooded individual began speaking to him.

"Doctor," it said, "I've hacked the TARDIS's telepathic interface to have a word with you. I'm transporting your consciousness to the TARDIS main interface now." The Doctor suddenly found himself back in his beloved TARDIS. The individual who first stole the TARDIS was propped up against one of the rails.

"I've brought you here tell you a few things," it said. "Firstly, the Sontarans are not working with me, or at least they think they are. Whatever you do, don't let them get a hold of me."

"Why shouldn't I," the Doctor retorted." You took my TARDIS, got my best friend's wife killed..."

"Amelia Pond is by all means still alive," the entity interrupted. "And this thing you call the 'Darkness' is something that both of us are fighting against."

The Doctor stared at the hooded person and thought. He immediately came to a realization, something that the person answered before the Doctor could.

"Your TARDIS has a consciousness, does it not? You've seen being of pure energy speak through different means. Surely, you are not going to stand there and denounce my existence. You even saw the Devil himself. Now ask the question."

The Doctor pondered for a moment and decided that what he thought was right and wrong wasn't important.

"What are you?" the Doctor finally inquired.

"I'm the living, breathing version of what you call the Universe," answered the Universe.


	7. Chapter Six- Perception

Disclaimer: I in no way, shape, or form own the _Doctor Who _series and the _characters _therein.

A/N- This will be my first try at doing fan fiction. Please read other chapters before coming to a conclusion.

**Chapter Six- Perception**

"Either choice I make," the Doctor said, "the Darkness is defeated." He had just regained consciousness as the Universe had severed the telepathic link to the TARDIS. The Doctor still had an after image of its interior in his head; it pained him to not be able to touch the controls. Yet with renewed vigor, he jumped up off the floor and ran out of the house.

"Wait!" Rory called out to the Doctor. "Amy said that you accidentally threw this with the bags." He walked over to the Doctor and handed him the pouch that he had received from the mysterious man all those years ago.

"Thanks…" the Doctor said with nostalgia as he grabbed Jenny's arm and took off towards the nearest police station.

"Why a police station," Jenny asked.

"Well, humans always find authority in someone packing a gun and I hope to find someone I know at this station because frankly," the Doctor said as he ran out of breath, "I think we are back in Cardiff, Wales." The Doctor finished his sentence just as he reached the door.

People were not even slightly surprised but the Doctor's strange attire. They were to busy filing complaints to the robotic officers or the man at the front desk. The Doctor tried yelling over the noise to get someone to help him.

"Doctor," Jenny said as she looked around," I don't think we're going to make any progress." He pondered what she said and began making adjustments to his sonic cane. He activated it, causing a sonic frequency to emit from it. Everyone turned a looked for the source of the sound soon setting their eyes on the Doctor.

"Hello," the Doctor said timidly," I'm the Doctor and I need some help." No one seemed to listen, that is except for one officer. The Doctor and Jenny walked over to the man. He reached out for the Doctor's hand and, surprisingly, the Doctor shook it.

"It's good to see you again…Mickey," the Doctor said. Mickey gestured the Doctor and Jenny to his office. The Doctor gave his daughter his seat as Mickey took his own.

"Doctor," Mickey began," things here are not as they seem." He put his hand out, stopping the Doctor from interrupting him. "About ten years ago, almost everyone on Earth experienced a blank spot in their memory. I felt something change but I couldn't put my finger on it." The Doctor wasn't paying any attention, instead, his eyes were focused solely on the static-like ripple in the corner of the wall.

"You see it, don't you Doctor…" Mickey said as he got up from his chair and walked towards it. "Everything in this world is wrong. The physics and fabric of it are all made up." He stood and rubbed his hand together nervously. "What does it mean?"

The Doctor leaned towards Jenny and whispered a few words into her ear. She in turn pulled her sonic pistol out and closed the blinds. The Doctor took his cane and gingerly and went towards the static spot. As soon as the cane got to the spot it didn't stop, instead, it went straight through it.

"Mickey," the Doctor asked, "how long have those robotic cops been here?"

"Come think of it, they were here a day after the event." The Doctor began pacing the room. "I'm missing something." He stopped talking to look at Jenny, who pointed at the window. "What else is going on?"

"Well," Mickey said to the Doctor, "we are getting reports of power fluctuations everyday. Communication reception is actually spotty even with our technology. We tried to work with the power and telecommunication companies, but the detectives on the cases just mysteriously lost interest in it. I didn't, so the commissioner just moved me to domestic cases."

"Whatever is going on," the Doctor said, "I think that we have been enveloped in a very elaborate perception filter." With that realization, Jenny saw the robotic cops for what they actually were.

"Doctor," she said, "these robots are Cybermen."


	8. Chapter Seven- Coming Home

Disclaimer: I in no way, shape, or form own the _Doctor Who _series and the _characters _therein.

A/N- This will be my first try at doing fan fiction. Please read other chapters before making a review.

**Chapter Seven- Coming Back**

"Doctor," Mickey said as he began unlocking the gun cabinet in his office, "we need to get to that relay station and shut down the broadcast." he took out a blue-colored rifle and turned it on.

The Doctor made a few adjustments to his sonic cane. "I hope those officers outside have the same weapons you do," the Doctor said as he activated the cane.

Jenny looked outside the window and saw that the people could truly see what the robots and even some of the officers truly were. People began screaming and running out as the Cybermen began immobilizing the citizens that were trying to escape. Other officers came from nowhere and formed a firing line at the back. Jenny stepped out and killed two Cybermen before they could fire on the officers.

"Who are those people Captain," one of the officers asked.

"This is the Doctor and his daughter," Mickey told them. "He's with us." The remaining policemen, the Doctor and Jenny, and Mickey made their way to the parking bay. Jenny got in one of the squadcraft and spliced the repulsorlift generator, causing the safety protocols to shut down.

The Doctor got in used his sonic to reveal the safety belts, which he put on. He activated the communication system on the craft and used his cane to boost the reception. Mickey came over the speaker with some news.

"Doctor," he said, "we need to get to that Skylane. We got reports of some sort of shield coming online over the broadcast tower. Are you ready?"

"Ready as I'll ever be," the Doctor said. The vehicles were soon off the ground and soaring off towards the outskirts of London.

"Doctor…" Jenny said to him, "I've always wanted to go on an adventured with you." The Doctor said nothing and instead tighten his safety harness. She continued talking regardless. "I lived by the only thing that I heard you say: 'A man who wouldn't.'. For such a long time, I traveled the galaxy searching for some way to find you. I was soon able to outfit temporal engines onto my rocket, but really all I wanted was…"

She was interrupted by an explosion that happened on the craft in front of them. Two flying robots threw the car down from the sky. The Doctor came up out of his seat.

"Since when do Cybermen fly," he yelled over the speakers as a laser beam shot the hat off of his head. The officers soon started returning fire as the whole Skylane was lit up with fire.

"Doctor," Mickey said over the comms system, "we can't keep this up much longer. London UNIT has mobilized and are fighting their way to the tower. That shield is almost seventy-eight percent up. ETA is in ninety seconds."

"Dad," Jenny shouted, "drive!" The Doctor couldn't refuse since she had already started unlatching the belts. He hastily took the control sticks and began driving.

"You know," the Doctor said, yelling above the noise of the lasers firing, "I never got my license renewed."

"Just drive!" she growled as she shot a Cyberman off the side of the cruiser. The Doctor now could clearly see the shields as they almost encompassed the top of the tower. "We can't get in!" Mickey told the Doctor through the comms system. Then an idea came to his mind.

"Reroute the shields to the front!" he yelled. The cruisers came closer and closer to the shields. "Brace for impact!"

The cruisers were within yards of the shields, the Doctor yelled only one word before they hit the shield.

"Geronimo!" the Doctor yelled as the cruiser hit the shield.


	9. Chapter Eight- Sacrifice

Disclaimer: I in no way, shape, or form own the _Doctor Who _series and the _characters _therein.

A/N- This will be my first try at doing fan fiction. Please read other chapters before making a review.

**Chapter Eight- Sacrifice**

The Doctor fought to keep the cruiser in the air as the electronics went haywire. The shields wiped out all navigational memory in the vehicles, making the automatic controls useless. The cruiser could barely stay in a straight line, as it soon made a b-line toward the wall of the facility. He switched the shields to full coverage right as it penetrated the walls.

The Doctor woke up groggy and disoriented. He could hear the shouts of the officers and UNIT soldiers fighting off the security bots. He soon saw his daughter's face in front of him. Jenny began shaking him to wake him up. "We have to move!" she shouted to the Doctor as he started waking up.

He got up as fast as he could and adjusted to his surroundings. Mickey and the others were pinned down in the room across from them. Smoke and the bodies of soldiers and Cybermen alike were strewn all over the floor. A sign on the wall read "Control Room: Floor 55".

"Jenny," he said, " we need to get to Floor 55." Jenny's response was interrupted by an explosion that rendered her unconscious. "Mickey!" the Doctor shouted, "get her out of her." Mickey grabbed her and pulled her into the control room right as the Doctor hacked the explosive doors.

"Well, the Doctor said, "We're stuck in here." He walked over to one of the many computers and began toying with it.

"Doctor," Mickey said as he rigged the door with a portable shield, "we're not getting out of here. We can still shut it down, but there's no way we can get out. The Doctor turned and looked at a gate-like device. To the left of it was a technician who was clutching her lower abdomen.

The Doctor approached her and applied pressure to the wound. She coughed up some more blood before the Doctor could begin speaking to her.

"How do we shut the relay off?" he asked. She looked at him and began shaking her head. After that, she just placed her hand on the back of the gate. Then she began speaking.

"This is a recreation of the Immortality Gate," she said before she began wheezing up more blood. "They made it…for you." The Doctor watched as she reached for a touchpad and handed it to him. "Power has to be diverted from the relay to the gate. From there every normal human life form is returned to a destination of its choosing."

"What about nonhumans," the Doctor asked her. She looked into his eyes and began speaking into the distance.

"My mother told me I would meet you…Donna Noble was her name. Doctor, if you go into that gate, you'll be subjected to the full effects of the Time Vortex. You'll be able to travel through it, but without navigation."

"But how do I shut off the perception filter?"

"You have to reroute power manually with the wires into the gate. That will require the blast shields to come up and the Cybermen to come in. You'll…you'll find that which was lost…" Her eyes looked past the Doctor and her grip on his hand loosened. Mickey and the others just looked at the Doctor; he just stood there pondering what he had to do.

Suddenly he came to a decision. He found the wires that were hooked into the relay and pulled them out. Mickey yelled as the gate started going up and the Cybermen could be seen. He ran to the Doctor and tried to talk some sense into him.

"Doctor, you have to stop!" he yelled as the soldiers set up defensive perimeters. The Doctor ignored him and began connecting the cables into their respective receptacles.

"Stop, or I'll shoot." Mickey put Jenny's sonic pistol to the Doctor's head. The Doctor calmly moved it out of his face. "Get your men out of here."

Mickey began ushering them into the gate, telling them to think of UNIT HQ as the location they wanted to go to. He made them put their weapons up against the wall. Soon, it was just Jenny, Mickey, and the Doctor.

"Well, aren't you going?" the Doctor asked as he pointed to the gate. Mickey responded by picking up a rifle. "Find your friend," he told him, "and when you come back, she'll be safe."

The Doctor walked over to his daughter and took her time-travel device off of her arm and onto his. He walked over to the Immortality Gate and took one last look at the body of Donna Noble's daughter. With one last breath, he took a few steps forward and entered the Time Vortex.


	10. Chapter Nine- My Raggedy Doctor

Disclaimer: I in no way, shape, or form own the _Doctor Who _series and the _characters _therein.

A/N- This will be my first try at doing fan fiction. Please read other chapters before making a review.

**Chapter Nine- My Raggedy Doctor **

The Doctor flew through the Time Vortex with only the protection of the bubble emitted by Jenny's device. He could catch slight glimpses of the past, present, and what would come. Soon he came closer and closer to what looked like London. He exited the Time Vortex and appeared in an attic. Once again, the Doctor's clothes were smoking. The strong smell of ozone drew him to his senses.

He looked down at his device and felt a cold chill as he read the date.

"9/2/1666," he said aloud. "The day that London began to burn…" It was ten o'clock at night, and by the Doctor's calculations, he only had two hours to find Amy before the whole city was in flames.

"Who're you?" said a voice. The Doctor turned around and looked down the barrel of a musket rifle. The Doctor instantly took out his wallet and showed his credentials. The man instantly put his rifle down and saluted him.

"Have you seen or met any strange people?" the Doctor said as the man led him out of the attic.

"Well Inspector," he answered, "the baker on Pudding Lane got a new maidservant. They said she appeared from nowhere with strange clothes on. Mr. Farriner received her with open arms." He led the Doctor outside and pointed down the street. The Doctor thanked him and went on his way.

The Doctor could feel that something wasn't right. When he looked down at the device, it was already five minutes to twelve. He ran to the bakery and walked in on a scary sight. Slumped in a chair was Amelia Pond dressed in the uniform of a maid. She held her time-traveling device in her left hand. Some life came back to her eyes as she looked at the Doctor.

"What happened," he asked her as he got her out of the chair. She looked at him and smiled.

"My raggedy Doctor," she said as he tried to take her outside. As soon as he put his hand out to balance himself a ripple appeared in the air and extended outward.

"The magic of time. isn't wonderful Doctor?" a voice spat behind the Doctor. The voice was one that he hoped he would never hear again. The Doctor slowly turned and looked at the new body of his archenemy, Davros. He had a Dalek-like blaster in one hand and a time-locking device in the other hand.

"You will burn here with your friend, as you left me to burn all those years ago." he lit a fire in one of the ovens and disappeared with a laugh. Soon, the whole place was in flames. The Doctor could hear the screams of the family who occupied the house. He set Amy back in the chair and began helping them out of the window. He knew that they could escape the time lock but he and Amy couldn't.

He went back to Amy and cradled her in his arms. Every time he pressed the button on the travel device, the readout went black. "If I die here," she told the Doctor with tears coming out of her eyes, "I'm glad that I'll be dying with you." As the fire came closer she clenched his hand as tight as she could. Finally, they both closed their eyes and waited for the end to come.

They both opened their eyes and found themselves back in front of the Immortality Gate.


	11. Chapter Ten- Gone

Disclaimer: I in no way, shape, or form own the _Doctor Who _series and the _characters _therein.

A/N- This will be my first try at doing fan fiction. Please read other chapters before making a review.

**Chapter Ten- Gone**

The Doctor turned and saw only Jenny propped up against the wall. Amy limped over to her while the Doctor looked for Mickey. Amy whistled to get his attention and pointed to the wires near the gate. He slowly made his way there. With each step, he hoped that what he would indeed be another technician and not Mickey.

Mickey lay dead on the floor with a mass of wires in his hands. He had holes in him where the lasers penetrated his body. The Doctor slid his hands down Mickey's face to close his eyes.

"Doctor," Amy said, "we need to get back to Rory." He walked over and put Jenny on his shoulder and began walking out. People were running and screaming as they fled the city. The little group just walked against the mass of people leaving the neighborhood.

When Rory saw Amy with the Doctor, he ran towards her and hugged her. They kissed and embraced each other for a bit while the Doctor silently put Jenny down on the kitchen table. Rory ran inside with Amy in hand and went to the Doctor's side.

"I didn't have the chance to ask you who this was ," Rory said as he fetched his medical kit.

"This is my daughter, Jenny." he answered as he sat down and put his face in his hands. "I've lost too many people." Amy sat in front of him and began talking.

"When you threw us out of the TARDIS, I could only stand and watch as it disappeared. I wanted to stay there and wait for you to come back. We eventually move on after that; ten whole years and I still couldn't forget you. And then the event happened, and everyone sort of just went on after that." she turned and looked at Rory, who was still attending to Jenny's wounds.

"Then UNIT showed up," the Doctor said as he began fiddling with his broken cane.

"They did," she told him as she began making a pot of. "They said that they figured out a way to recreate the technology of the TARDIS in a compact form. I joined on the project and helped as much I could until we finally got it to work. Colonel Dorian, who was over the project, handed me a black box that contained the device. From there, I went into a special chamber where I was told to activate the device."

"This is where Jenny's handheld came into existence." The Doctor said this to Amy as he showed her the insides of both devices. "They're almost identical except for better components." Amy walked over and handed the Doctor his cup of tea. The Doctor finished her story before she could.

"Davros, the Daleks, the Cybermen, and the Sontarans literally want to capture the Universe." the Doctor said to Amy after filling in the blanks of her story. "I should've never kept you with me as long as I did. I'm endangering you even now." As he was getting up, he knocked over a brown satchel.

An odd multicolored device with odd writing fell out with a thump. The Doctor stopped where he was and bent down to pick it up. He flashed back to the moment he was handed the bag.

"What is that thing?" Rory Pond said as the device began to glow. The Doctor took one look at it and recognized it strangely as part of the TARDIS. A note with a single word on it felt out.

"What does it say," Jenny asked the Doctor as she began tried to get up.

"TARDIS," the Doctor read out loud as he disappeared in a flash of light.


	12. Chapter Eleven- Confrontation

Disclaimer: I in no way, shape, or form own the _Doctor Who _series or the _characters_ therein.

A/N: Please give reviews so I will have an idea if I should continue writing in the current style or not.

**Chapter Eleven- Confrontation**

The Doctor opened his eyes and found himself back in the TARDIS. The "Universe" was at the controls tapping at a readout on the monitor. "Hello Doctor," he said without looking at him. "It appears that fate is more powerful than you realize." He pulled on of the knobs on the console and leaned up against a rail.

"Why does taking the TARDIS have to do with the Darkness?" The Doctor asked as he began walking over to the controls.

"The Darkness," he answered, "needed something of its own to follow. This TARDIS has apparently became a symbol or beacon of sorts in the Universe. The Darkness, my Doctor, isn't some celestial phenomenon for it is of actual intelligence. This alliance of evil that you are no doubt thinking of at this very moment has been whispered to and prodded by the forerunners of the Darkness."

"Then why didn't you say that in the first place?" the Doctor sneered at the Universe in a scream.

"Because you would've never believed any of it. You would've reacted just as skeptical as you are now."

The Doctor began fooling with the controls as the Universe tried to stop him. "This isn't skepticism," the Doctor barked as the Universe tried to stop him. "This is me taking back what is rightfully mine!" He pressed the button to turn off the gravity and pushed the Universe away from the controls.

"You wouldn't," the Universe yelled as the Doctor set course for the three interconnected rocks that held the Shadow Proclamation. The Doctor began locking the controls as the Universe got a hold of him. He hit the Doctor and sent him flying over the console, causing all sorts of knobs and switches to be moved. All safety protocols on the TARDIS were then turned on.

"We're going to die because of you!" The Doctor yelled at the Universe as the TARDIS came hurling into Shadow Proclamation airspace. The TARDIS crashed into one of the buildings causing the Judoon soldiers to come out and surround the wreckage.

"Don't do this Doctor." The Doctor opened the TARDIS doors and pointed to the Universe, who was on the floor. "Don't let them take me!"

"You're the powerful one, save yourself." The Doctor said these last words and walked back inside his TARDIS. Before he could leave, he was stopped by a women who wore a white veil over her face.

"You are herby summoned to attend the trial of Subject 266." She said this while she motioned to the Universe. "I'm curious though as to the fact that this individual calls itself the Universe."

"If I told you, you'd never believe me." The Doctor held the women's hand, nodded, and then proceeded to return to Cardiff to get his daughter and the Ponds.

As he stepped out of the TARDIS and into the living room of the Pond's he could hear Amy and Jenny arguing.

"He isn't the Doctor you used to know!" Jenny said as the Doctor stepped out of the TARDIS. They just stopped and looked at him. Jenny went inside the TARDIS and the Doctor went also. Amy put her hands on the Doctor's shoulder. "Don't become the thing you've been fighting." She kissed the Doctor's cheek and walked into another room.

"Why are we going back," Jenny asked as the Doctor slowly shut the door on the TARDIS. The Doctor began activating the controls. "Something doesn't seem right, Jenny. If he was all powerful, then why didn't he fight back? He could've vaporized everything around him if he was in danger, but he didn't." The Doctor set the TARDIS for a slow course to the Shadow Proclamation.

Jenny sat on the floor of the TARDIS with her hand to her head. She was thinking about the mysterious individual as much as the Doctor was. Of all the years that the Doctor had traveled through space, not once had he heard of anything called the "Darkness" or a living manifestation of the Universe.

Soon, Jenny was sound asleep. The Doctor carried her into one of the bedrooms and put a cover over her. Her wrote a note and set it down on the command console before he stepped outside to meet the Judoon soldiers. They led him into an ornate living area that was painted completely white. All the furniture was grey. The woman that Doctor had met before he left was standing at a window, looking out into space.

"It's beautiful," she began, "in all aspects that make beauty what it is. All my life I've wanted to travel this Universe, but my job here stops me."

"I guess you're the new Shadow Architect," the Doctor inferred as he fooled with his sonic screwdriver. "Nevertheless, I need to see the prisoner before trial." The Shadow Architect pressed a button on a console, transporting them into a holding area. The Door was guarded, not by Judoon, but by five heavily armored humanoids.

"Doctor, are you prepared?" The Doctor simply nodded yes, and she opened the door into the interrogation room.


	13. Chapter Twelve- One Simple Choice

Disclaimer: I in no way, shape, or form own the _Doctor Who _series and the _characters _therein.

A/N- This will be my first try at doing fan fiction. Please read other chapters before making a review.

**Chapter Twelve- One Simple Choice**

The Doctor walked in at a deliberate pace and sat down in the chair. The man just looked at him with his color changing eyes. "You've brought it here," the Universe said. "The Darkness will come here for me.

"Why should I care," the Doctor counter. "You've done nothing but gave me pain and suffering. If you are the Universe, I've constantly traveled you saving you from all sorts of destruction. When I asked something of you, you never gave it to me." The Doctor and the Universe locked eyes and stared at each other.

"You're still alive, aren't you?" the Universe asked. "The four knocks haven't been heard, have they. You are still alive because of me, nothing more and nothing less."

"Then tell me what the Darkness is!" the Doctor slammed his fist down on the table in anger.

"It's everything that you've been running from." He got right up in the Doctor's face and began pleading. "It is coming for you, Doctor. I am the only one that can save you, but you have to let me go."

"What happened to not making deals?" the Doctor could hear all the times that he tried to bargain and reason with the Universe, all of which he had never gotten what he wanted.

"You can either save me right now or put me on trial. It is, in essence, a simple choice to make." The Doctor leaned towards the Universe and whispered something in his ear. He said nothing and nodded. The Doctor took his seat and went to the door.

"What did he say to you?" the Shadow Architect asked the Doctor as he took a seat in the atrium. Somehow, the Doctor knew that the old Shadow Architect didn't exactly give up her seat on purpose.

"He said…" the Doctor paused as he carefully picked over his words, "what needed to be said." The Shadow Architect stood with a puzzled look on her face. Finally, she sighed and left the Doctor alone.

_**(Earth, the Pond's Residence, after the Doctor's departure using the device)**_

Unbeknownst to Rory or the Doctor, Amelia Pond was dying. Her body had received too much of the emissions of the Time Vortex. The various particles had bombarded her body since the time device had no sort of shielding technology sophisticated enough to protect her. The only person to know of this was Jenny, whom she talked to after the Doctor had disappeared.

Jenny lay on the table breathing calmly. When she heard Amy sit down next to her, she slowly propped herself up and began speaking.

"Are you alright?" Jenny asked when she Amy put her hand to her chest. For a moment, Amy debated whether she should tell Jenny. Being that she was the Doctor's daughter though, she made up her mind.

"I'm dying," she told Jenny pointblank. Jenny slowly started crying. "Why am I crying?" she asked Amy. "I don't know why I'm crying." Amy soon started tearing up herself. Soon, both of them were crying their hearts out.

"Give the Doctor this note when you think he is ready," Amy said to Jenny as she prepared to leave. Jenny took the note and put it in her vest pocket. Before she could leave though, Rory walked. "Where are you going," he asked with a quiet voice.

"I'm going to help the Doctor," she answered.

"That's what got us into this mess into the first place." His eyes momentarily flashed with anger. "You just don't understand do you," he continued, "that he doesn't need our help anymore. He never did." Rory was preparing to walk back to the living room when Amy told him. "I'm dying!" Rory's face was completely pale. What she was getting ready to do came to him.

"I don't want any part of this," he said after he kissed his wife for the last time. As he walked out, Jenny shouted at him.

"He isn't the Doctor you used to know!" Jenny said as the Doctor stepped out of the TARDIS. They just stopped and looked at him. Jenny went inside the TARDIS and the Doctor went also. Amy put her hands on the Doctor's shoulder. "Don't become the thing you've been fighting." She kissed the Doctor's cheek and walked into another room.

When she heard that the TARDIS had left, she walked outside and got into a car. She drove the few or so miles to UNIT headquarters. Past a military checkpoint, she parked her car and walked through the revolving doors into the courtyard. From there she made her way to Colonel Dorian's laboratory.

"Mrs. Pond, what brings you here?" he asked as he began putting another one of the time-traveling devices back into a protective case. "I'm going to need that," she told him.

"You very well know that I cannot let you do that." He continued working, ignoring one important fact.

"Then you haven't seen what I have in my hand." He carefully turned and saw that Amy had a pistol in her hand.


	14. Chapter Thirteen- Darkness Revealed

Disclaimer: I in no way, shape, or form own the _Doctor Who _series and the _characters _therein.

A/N- This will be my first try at doing fan fiction. Please read other chapters before making a review. Also, please tell me if you like the new story setup-(One character to another with something to get link the events together.)

**Chapter Thirteen- Darkness Revealed**

_**(Shadow Proclamation exterior) **_

"The trial's starting," a voice said. The Doctor turned and watched as a messenger went to each person and told them the news. One by one, they stopped what they were doing and followed the man to the exit. He slowly walked away from the pillar he was propped up against and stayed a few paces behind the crowd.

As the crowd entered the large courtroom, the Doctor tensed. The last time he was in this place, he was on trial. The thought of being back in here sickened him, but he had to. Soon, everyone was seated and proceedings began.

"As of Clause 374 of Shadow Proclamation, this individual is on trial for the unsanctioned taking of a Type 40 TARDIS belonging to the Doctor. Since deadly force was unnecessary, the entity has requested that we present what evidence we have against him and allow him to speak shortly before his sentencing." The Shadow Architect addressed the crowd from the middle of the courtroom. The Universe was seated in front of her surrounded by guards.

The room soon darkened. A holographic screen came up with photos of burning planets. "These are locations that the TARDIS was spotted at. These pictures were taken soon after it left. You were also found inside of the TARDIS with a visibly injured Doctor on the floor. Your DNA cannot be confirmed on our databases, and your presence here has affected our devices."

The Universe wasn't paying attention though. The Doctor got up when he saw the Universe whisper Pond. He got up and began making his way past the guards. Halfway there, and guards were already trying to subdue him. The Shadow Architect stopped them. The Doctor took out his sonic screwdriver and revealed none other than Amelia Pond.

"I'm sorry, she said as she disappeared."

_**(UNIT Headquarters)-Five minutes before trial…**_

"You can put the gun down," Colonel Dorian said to Amy as she led him through the hallways. He commanded the soldiers to lower their weapons as they made their way to the test room. After a few more minutes of walking, Amy pushed him past the door, and broke the opening mechanism.

"Take it out," she yelled as she aimed the gun at his temple. Colonel Dorian cautiously undid the clasps and locks on the case until he finally held the device in his hand. "Now type in your authentication code," she yelled. He called for the keypad to come out of the device. He slowly input the twenty-five digit authentication code and handed it to her.

"Thanks," she told him as she shot his knee. The soldiers were already trying to open the door as she was dialing in a sequence of numbers that came to her mind. An anti-material laser rifle was set at the door, ready to fire at her. In one split second, she disappeared in a flash of white light just as the beam penetrated the door.

Amy looked and found herself in bus. She could see a blue suited individual in a brown trench coat walking towards the TARDIS. He had a sad look on his face, as if he lost a family member. "This was the Doctor before the one I know…" she said as she faded out again. She then found herself in front of a shackled individual in the middle of a courtroom. She looked into his eyes and found that they changed color. He smiled at her and began speaking to her, not with his mouth, but with his mind.

"Hello Amelia," the Universe said to her as its trial started. Amy looked around and saw that no one could see her. Steadily, the pain in her heart got worse as she stood there. "I need to know what will happen to the Doctor." The Universe just looked at her and shook his head with sadness. "For your coming death, I am so sorry that you have to die like this. Follow your letter's instructions to the exact word, and I will make sure that he gets to see you one last time."

"Pond." he murmured out loud. Amy looked and saw a commotion in the upper seats as a man made his way to the center. Amy Pond watched as the Doctor took his sonic screwdriver out of his suit-pocket. The Doctor's face showed confusion as she said the only words that came to mind. "I'm sorry," she said as she disappeared. Mass panic then ensued. All of the doors and windows imploded as the Darkness came flying in.

The Doctor stood unafraid in complete darkness. He held his screwdriver away from him and turned a simple light on, causing the Darkness to wither away and reveal the true nature of its intentions.


	15. Chapter Fourteen- The Moment of Truth

Disclaimer: I in no way, shape, or form own the _Doctor Who _series and the _characters _therein.

A/N- This will be my first try at doing fan fiction. Please read other chapters before making a review.

**Chapter Fourteen- The Moment of Truth**

All around the chamber stood the Alliance of the Doctor's enemies. Slitheen, along with Daleks, Davros, and other creatures stood in the chamber. Lights from various spaceships shined through what was left of the windows. An Atraxi eyestalk could be seen peering in from the outside.

"Give him to us Doctor, and we will spare you." Davros began stepping towards the Universe. He was stopped by the Doctor's hand.

"You will not touch him," the Doctor said as he pointed his sonic screwdriver at Davros's head. Davros backed away and motioned at the Shadow Architect. The Darkness suddenly flew into her mouth, causing her to double over. When she looked up, her eyes were completely black. When she spoke, her voice was not her own.

"I am that which you fear." the Darkness hissed at the Doctor. "I am everything that men fear." Her hand pointed to a group of people cowering in the seats. A black substance came forth from her hand and into their ears. They screamed for a few seconds, and then fell over dead. "This is true power, Doctor. Power, that you will no doubt experience first hand if you do not give him to me."

The Doctor stood still. He slowly lowered his arm and deactivated his sonic screwdriver and began speaking in a tone that was quiet at first, but got louder as the Doctor began to get angry.

"I am the Oncoming Storm. Whole star-systems know my name. I am the Watcher and Keeper of Time. I alone am the Champion of Time. I am the Destroyer of Worlds!"

Before the Darkness could answer him, a large piece of glass fell from the ceiling. A single lone figure dropped down into the fray and right pass Davros's shield. The Doctor looked as his own daughter attached an explosive device onto Davros's back, and pushed him towards a group of guards. She tackled the Doctor right as the device detonated. Soldiers from other star-systems blasted through the doors and began engaging the Sontarans and other hostile races of the Alliance.

Jenny defending the prisoner with what appeared to be the Master's laser screwdriver as the Doctor went after the Darkness. "You will most certainly die trying to capture me." it yelled as the Doctor chased it through the halls. Soon, they were outside. The spacecraft above them were doing battle. Blasts from different weapons hit and made whole building collapse on themselves. Blasts of electricity from the Atraxi hit different soldiers and vaporized them on the spot. Daleks could be seen swarming all over the hulls of other ships.

The Darkness stood laughing at it all. "Look at what you have created," it said to him. "Every single one of the choices you have made has led us to this moment." In his head, the Doctor could see all of the decisions he had made and regretted making. "No." he said to the Darkness as it came towards him.

"One simple choice." the Doctor heard this single phrase spoken in his head. He looked past the Darkness and realized what he had to do. He ran at the Darkness, taking it by surprise. He tackled it right off of the rails of the balcony and down the 200 stories of the main spire.

The body that the Darkness was in took most of the damage of the impact. Since gravity on the rocks was slightly different, the fall wasn't as dangerous. Yet, as the Doctor rolled off of the body, he could feel blood running out of his mouth. His breathing was labored from the broken ribs he had sustained from the fall.

"You…you…couldn't have." the Darkness said as a bright light appeared near the Doctor. A red cloaked figure came out of the light and pulled the Darkness straight from the Shadow Architect's body. The Doctor recognized the face of that belonging to the Universe. "Doctor," he started, "I didn't think you would do it."

The Doctor gave the biggest smile he could muster and coughed up some more blood into his hand. The Universe walked over to him and said, "I'll give you back that which you gave to me." He put his hand on the Doctor's hearts and gave back the regeneration energy that he took from him. The Doctor's wounds slowly faded away until he was at full health. He got up and shook that Universe's hand.

"What will happen now?" the Doctor asked.

"The forces of the Alliance will be driven away from here and attacked senselessly as the make this retreat. I will take this entity and put it in the safest place I know. You, on the other hand, have one more trip to make." The Universe gave the Doctor one last nod and disappeared with a wave of his hand.

He turned back around and saw the TARDIS in front of him. It opened the door on its own, prompting the Doctor to run inside. The door closed behind him and the controls on the panel started operating on their own. "This is still my TARDIS," the Doctor whispered as the controls stopped moving. The door opened again on its own, and the Doctor stepped outside to see where he was.


	16. Chapter Fifteen- Amelia

Disclaimer: I in no way, shape, or form own the _Doctor Who _series and the _characters _therein.

A/N- This will be my first try at doing fan fiction. Please read other chapters before making a review.

**Thanks to everyone who took their time to read this and all of the other chapters, for it is in the interest of the reader that makes doing this worthwhile.**

_**Chapter Fifteen- Amelia**_

Amelia Pond was not use to this kind of pain. As the time traveling device shattered in front of her feet, she felt a sense of unfulfillment about her life; there were still things that she wanted to say to the Doctor. The problem was that she didn't know if she would ever have that chance.

As she looked around, she didn't realize where she was. She stood in the middle of a vast and beautiful garden. The people in it looked human enough, but something about the sky didn't seem right. "It doesn't matter," she thought as she took a seat beside an old man.

"It takes a very determined person to find tranquility," he said to her with a smile on his face. "What do you mean?" Amy asked with a puzzled expression on her face. The old man chuckled and put his hand into a brown paper bag and flung some seeds to the birds that had gathered at his feet. He stopped and stared off into the distance before he continued talking.

"Then you don't know what this place is, do you?" The old man unscrewed the top off of a prescription drug container and took out two pills that he swallowed with a drink from his Thermos. "Ma'am, this is the Garden of Tranquility and people come here when they are prepared to die." Amelia felt as if she should be afraid, but somehow she knew that he meant no harm.

"What about the Doctor?" she said as tears began streaming down her face. The old man took out his handkerchief and slowly wiped the tears from her eyes. "You may have heard that the Universe makes deals with no individual, but this isn't always the case. When a special person like you comes along and gives up everything for something she believes in, it makes an exception."

Amelia felt a slight breeze touch her face, followed by a sound that she was all too accustomed to. The old man stood up with her and watched as the TARDIS materialized in front of them. The Doctor stepped outside of it and smiled when his eyes fell on Amelia. She said nothing as she ran to him and hugged him as tightly as she could.

"You came," she whispered softly as he held on to her. "That moment after the prison ship fiasco…you said you'd see us…" He slowly moved his finger to her mouth and stopped her midsentence. "Always remember that…" "…the Doctor lies." She finished his sentence for him.

"I'm so sorry for this." Amelia Pond said as she closed her eyes and fell to the ground. "Someone save her!" the Doctor shouted as white clothed people came to her aid. "You have to help her!" The paramedics tried in vain to being her back. They soon stopped and shook their heads in sorrow. The Doctor could feel as Amy's hand slipped into his own.

"My…raggedy…Doctor…" she murmured with a smile on her face as she stopped breathing completely.

"No!" the Doctor shouted with grief. "No, no, no, no, no, no, no, no!" The Doctor cradled her body in his arms, rocking her gently back and forth. With his hand, he slowly caressed her face and rubbed his hand through her hair. The Doctor turned and looked at the old man whom Amelia conversed with. He stood completely still; his face was blank with emotion save for the one tear that ran down his wrinkled face. He turned and looked directly at the Doctor and said, "It is done," before he turned around and faded into the air.

The Doctor lay Amelia Pond down on one of the benches and took off his suit. Draping it over her, he took the strange device out of the satchel and placed under Amy's hands. The Doctor stepped away and activated it with his sonic screwdriver. He remained still and watched as the bench and her body slowly disappeared into nothingness.

The Doctor stepped inside of the TARDIS and closed the doors behind him. He made a short walk to a chair and sat down in it. As the events of the day unfolded in his mind, a shiny object on the controls caught his eye.

Hanging from one of the knobs was a gold chain with a diamond ring attached to it. Propped in one of the crevices of the controls was a letter in an envelope. The front of it simply read "Doctor".

"_My Doctor_," it began…

"_I was never fond of saying goodbye. To me, a farewell represents some sort of defeat. I must sadly and with great bitterness accept this defeat, for death is a defeat that few escape from. Do not be sad and do not pity me. Pity everything that I have left behind, for that is all that the dead leave behind. I simply regret that I did not die with the man I loved with all of my heart. Rory knows that I will not return from this journey. The only thing I ask of you is to never forget who you are. I waited for you and you came. Now it is your turn to wait for me…_

_ With great love,_

_ Amelia Pond_

After he read this letter, the Doctor was never seen again.

In the Scotland of the future, they tell of a small grouping of trees around a clearing that houses the graves of three people. Every year, a flash of light can be seen appearing through the branches of the tree. As fast as the light appears, it disappears after a few minutes. This entity always leaves a blue rose on the middle tombstone. The inscription on it reads "Amelia Pond: Born 1989- Died xxxx." Below that reads another inscription of words that reads "The Girl Who Waits No More."

To the right of hers is the tombstone of that which belongs to her husband Rory Pond while the one at the left of hers refers to a person simply known as the "Doctor". The inscription on his reads, "My Doctor…A Man Who Waits for Destiny."

A/N- The Doctor will return in the next installment of Series 1 called Destiny. The name of the book shall be given to you in a few days along with the first few chapters of it.


	17. Epilogue- A Contract for the Ages

Disclaimer: I in no way, shape, or form own the _Doctor Who _series and the _characters _therein.

A/N: **To everyone who has read this, I thank you. I cannot wait to bring you more of everyone's favorite Doctor. If you want to keep this adventure going, please favorite me. If you want to air your opinion or think I should change something, please review. I am now going to begin introducing OC characters into the books. **

**Epilogue- A Contract for the Ages**

_Many were uneasy by the disappearance of the Doctor. So, people began fleeing Earth in droves and going to other planets. With the influx of refuges, widespread panic across the Universe insured. Soon, everything went into turmoil. The various factions of the Alliance soon fractured after the battle in the Shadow Proclamation chambers. With the loss of Davros, the Daleks went into hiding in the very depths of the Universe. The Sontarans and Slitheen were cowering on their own planets, waiting for the right time to strike again._

_Searching for answers, the representatives of the various systems came to the Shadow Proclamation for answers. Instead of progress…they met their deaths. On the second day of negotiations, a series of explosions destroyed all three of the stones holding the Proclamation in place. From the ashes of the collapsed galactic government rose the__**Inquisitors**__. _

_**The Inquisitors were a group of the most powerful individuals in the Universe who saw a chance to take the place of government for themselves. Led by Grand Inquisitor Lucius Cross, they cemented their control instantly by seizing and conquering all of the major metropolises in the Universe. Then they sought to take over the whole planets themselves.**_

_**A planet undergoing "conversion" would go through something called an "Inquisition". The soldiers of the Inquisitors would crush, capture, and torture any opposition. From there, innocent people were branded as deadly "political opponents" and put to death in front of the masses. Any function and remaining form of government would be silently and swiftly eliminated. After that, an Inquisitorial Headquarters would be placed on the planet, sealing the planet's fate. As time passed, the Inquisition soon found itself entering other galaxies. Its influence spread like a cancer. The people had no choice but to believe all of the propaganda or perish.**_

_Meanwhile, in a remote spaceport on the edges of Andromeda Galaxy untouched by the Inquisition, life was still normal. The various captains and pilots of still hauled their loads to various locations under the auspices of armed escorts. To ease their nerves, the space-hardened travelers would all spend their R&R time at a gigantic cantina called "The Burning Rose". _

_Especially now, you could find many shady people to do business with inside. The establish was run by an Ood who insisted that people call him Greg. His bartenders were often robots who had lost their way or had been sold to the Ood by the crews of various ships. Like any good barkeep, Greg took great care of his "regulars". What they did was none of his business; as long as they kept paying for their drinks, they could do as they please. _

_Today was different though. He was instructed to give a note to one of his most loyal customers by a tall and masked individual. "Sir," the Ood said as he beckoned the man over. "I was instructed to give this not to you." The Caucasian human took the note and ripped the seal on it with a knife. "Thanks," the man said as he placed a bundle of credits on the counter and entered his usual backroom area. _

"_I know you're here," he yelled. "You can come out." The lights suddenly turned on, revealing masked individual. Along with his respiratory mask, he wore a black robes that completely concealed his body from the neck down. The individual held out his black gloved hands. _

"_You're a hard man to find." the man just focused on the individual's mask. Everything about the man suggested that he had a rich upbringing. The way he conversed, even with the mask on, proved this. "If you wanted someone to haul your riches somewhere safer, the freight captains are outside." He flourished his hand in the direction of the door at the same time he said "outside"._

"_**I can pay triple your normal rate…Morpheus." Morpheus froze and instantly thrust his laser screwdriver from his sleeve. "Apparently, I'm not doing my job well enough," Morpheus spat as he turned it on. **_

"_**Laser Screwdriver developed by Lazarus Industries," the man inquired as he stared directly into its barrel. He continued speaking as if nothing was wrong. "Six million credits for two separate contracts doesn't sound right, or what?" Morpheus stared at the man for a few more seconds until he retracted his screwdriver. Finally he asked the question that all assassins ask customers.**_

"_**Who are the marks?" The masked man merely smiled and said, "Grand Inquisitor Lucian Cross and the Doctor." **_

_**A/N- Work on Book 2 is beginning smoothly as planned. Don't forget to favorite me to stay updated on the series. Thanks for everything and I hope you enjoyed this first bit of fan fiction from me. (The bolded text above is important pieces of information in Book 2.)**_


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